The echo of underwater lidar often contains a significant amount of scattering clutters. In order to effectively suppress this scattering clutter and improve the ranging accuracy of underwater lidar, a novel denoising method based on complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) and wavelet threshold denoising is proposed.<br/>The CEEMDAN-wavelet threshold denoising algorithm uses the correlation coefficient to select Intrinsic Mode Function(IMF) components obtained from the CEEMDAN decomposition. IMFs which are more closely correlated to the original signal are selected. Then, the wavelet thresholding denoising algorithm is applied to each of the selected IMF to perform additional denoising. For each IMF component, specific threshold values are calculated based on their frequency and amplitude characteristics. Subsequently, the wavelet coefficients of the IMF components are processed using these threshold values. Finally, the denoised IMF components are combined and reconstructed to obtain the final denoised signal. Applying the wavelet threshold denoising algorithm to IMF components can effectively remove noise components that cannot be removed by traditional CEEMDAN partial reconstruction methods. By using threshold values calculated based on the characteristics of each IMF component, the wavelet thresholding denoising process has been improved compared to directly using a single threshold value. This approach enhances the algorithm's adaptability and enables more effective removal of noise from the signal.<br/>We applied the proposed method to underwater ranging experiments. A 532 nm intensity-modulated continuous wave laser was used as the light source. Ranging was performed for a target in a water with varying attenuation coefficients. A white polyvinyl chloride (PVC) reflector was used as the target. When directly using correlation extreme values to determine the delay at a distance of 3.75 attenuation lengths, it resulted in a ranging error of 19.2 cm. However, after applying the proposed method, the ranging error was reduced to 6.2 cm, the ranging accuracy was effectively improved. These results demonstrate that the method has a significant denoising effect in underwater lidar system.